Lineage analysis of astrocytes and ependymal cells from joint cortex (clusters 20, 2, 12, and 23)
Alexis Blanchet-Cohen
13 May, 2019
1 Setup
source("helper_functions.R")
library(cytokit)
library(ggedit)
library(kableExtra)
library(monocle)
library(patchwork)
library(readxl)
library(readr)
library(R.utils)
library(Seurat)
library(tidyverse)
library(viridis)sample <- c("joint_cortex.seurat")
tables_directory <- "tables"
dir.create(tables_directory, showWarnings = FALSE)
monocle_objects_directory <- "monocle_objects"
dir.create(monocle_objects_directory, showWarnings = FALSE)1.1 Load Seurat objects
input_directory <- "/mnt/KLEINMAN_SCRATCH/projects/sjessa/from_hydra/single_cell/2019-02_revision1/output/atlas-02"
load(file.path(input_directory, "joint_cortex.seurat.Rda"))
seurat <- joint_cortex1.2 Convert Seurat object to Monocle object.
selected_clusters <- c(20, 2, 12, 23)
selected_clusters <- paste0("^", selected_clusters, "-")
selected_clusters <- grep(paste(selected_clusters,collapse="|"), levels(seurat@ident), value=TRUE)
# Change cluster name
seurat@meta.data$cluster <- seurat@meta.data$cluster_joint
monocle <- seurat_to_monocle(seurat, selected_clusters)
monocle <- orderCells(monocle, reverse=FALSE)
colours <- monocle@experimentData@other$colours2 Monocle plots
2.1 Cell trajectories
p <- plot_cell_trajectory(monocle, color_by="cluster", show_branch_points=FALSE) + scale_color_manual(values=colours)
p <- p + theme(legend.title=element_blank())
show(p)
p <- p + facet_wrap(~cluster) + theme(legend.position = "none")
show(p)
plot_cell_trajectory(monocle, color_by="Pseudotime", show_branch_points = TRUE)
plot_cell_trajectory(monocle, color_by="State", show_branch_points=TRUE)
p <- plot_complex_cell_trajectory(monocle, color_by="cluster", show_branch_points=FALSE) + scale_color_manual(values=colours)
p <- p + theme(legend.title=element_blank())
show(p)
2.2 Differentially expressed genes across pseudotime
2.2.1 All genes
diff_test_res_all_genes <- differentialGeneTest(monocle,
fullModelFormulaStr = "~sm.ns(Pseudotime)", cores=12)sig_gene_names_all_genes <- row.names(subset(diff_test_res_all_genes, qval < 0.1))
plot_pseudotime_heatmap(monocle[sig_gene_names_all_genes,],
cores = 12,
num_clusters=1,
show_rownames = FALSE)
diff_test_res_all_genes <- diff_test_res_all_genes %>% rownames_to_column("gene")
write.table(diff_test_res_all_genes, file.path(tables_directory, "4-forebrain_astro_ependymal_joint_cortex_cluster_20_2_12_23_diff_test_res_all_genes.txt"), sep="\t", quote=FALSE, row.names = FALSE)2.2.2 Transcription factors
input_directory <- "/mnt/KLEINMAN_SCRATCH/projects/blancha/analyses/njabado/single_cell/annotation/animaltfdb3.0"
input_file <- "Mus_musculus_TF.txt"
transcription_factors <- read_tsv(file.path(input_directory, input_file), col_types = cols())2.2.2.1 Pseudotime heatmaps of significant transcription factors
2.2.2.1.1 q value < 5*10^-5
significant_genes_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, qval < 5*10^-5) %>% .$gene
cat("Number of significant genes: ", length(significant_genes_q_value_5_10_minus_5))## Number of significant genes: 3853significant_transcription_factors_q_value_5_10_minus_5 <- as.character(significant_genes_q_value_5_10_minus_5[significant_genes_q_value_5_10_minus_5 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_5_10_minus_5))## Number of significant transcription factors: 176plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=3, return_heatmap=TRUE, show_rownames = TRUE)
plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)
# The RMarkdown PDF has issues, hence this custom function to save the PDF file.
save_pheatmap_pdf(plot_genes_heatmap_output_q_value_5_10_minus_5[[2]], file.path("figures", "4-forebrain_astro_ependymal_joint_cortex_cluster_20_2_12_23", "diff_test_res_plots_transcription_factors_only_q_value_5_10_minus_5_heatmap_custom.pdf"), width=16, height=36)## pdf
## 2heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
ph_res_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[2]]
pheatmap_ordering_q_value_5_10_minus_5 <- rownames(heatmap_matrix_q_value_5_10_minus_5[ph_res_q_value_5_10_minus_5$tree_row[["order"]],])
transcription_factors_table_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_5_10_minus_5)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_5_10_minus_5 <- transcription_factors_table_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))
write.table(transcription_factors_table_q_value_5_10_minus_5, file.path(tables_directory, "4-forebrain_astro_ependymal_joint_cortex_cluster_20_2_12_23-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5.txt"), sep="\t", quote=FALSE, row.names=FALSE)
heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
heatmap_matrix_q_value_5_10_minus_5 <- as.data.frame(heatmap_matrix_q_value_5_10_minus_5) %>% rownames_to_column("gene")
heatmap_matrix_q_value_5_10_minus_5 <- heatmap_matrix_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))
heatmap_matrix_q_value_5_10_minus_5 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")| gene | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Nfix | 0.7322132 | 0.7553515 | 0.7783987 | 0.8012368 | 0.8237476 | 0.8458119 | 0.8673103 | 0.8881231 | 0.9081298 | 0.9272098 | 0.9452423 | 0.9621059 | 0.9776793 | 0.9918409 | 1.004469 | 1.015443 | 1.024640 | 1.0319395 | 1.0372210 | 1.0403638 | 1.0412481 | 1.0397547 | 1.0357653 | 1.0291624 | 1.0198298 | 1.0076524 | 0.9925165 | 0.9743101 | 0.9529227 | 0.9282460 | 0.9001737 | 0.8686018 | 0.8334289 | 0.7945561 | 0.7518878 | 0.7053314 | 0.6547978 | 0.6002015 | 0.5414611 | 0.4784993 | 0.4112434 | 0.3396254 | 0.2636509 | 0.1837346 | 0.1004371 | 0.0143125 | -0.0740920 | -0.1642379 | -0.2555952 | -0.3476435 | -0.4398724 | -0.5317817 | -0.6228816 | -0.7126928 | -0.8007462 | -0.8865829 | -0.9697536 | -1.0498181 | -1.1263446 | -1.1989087 | -1.2670927 | -1.3304844 | -1.3886753 | -1.4412600 | -1.4878339 | -1.5279919 | -1.5613260 | -1.5874242 | -1.6058672 | -1.6162272 | -1.6180645 | -1.6109258 | -1.5943459 | -1.5681458 | -1.5325936 | -1.4879816 | -1.4345901 | -1.3726893 | -1.3025414 | -1.2244025 | -1.1385248 | -1.0451580 | -0.9445513 | -0.8369551 | -0.7226222 | -0.6018097 | -0.4747803 | -0.3418030 | -0.2031554 | -0.0591235 | 0.0899964 | 0.2438969 | 0.4022595 | 0.5647529 | 0.7310331 | 0.9007430 | 1.0735115 | 1.2489539 | 1.4266713 | 1.6062509 |
| Dlx1 | 1.8000044 | 1.7705239 | 1.7411388 | 1.7117691 | 1.6823371 | 1.6527667 | 1.6229841 | 1.5929174 | 1.5624967 | 1.5316541 | 1.5003243 | 1.4684438 | 1.4359516 | 1.4027893 | 1.368901 | 1.334233 | 1.298734 | 1.2623585 | 1.2250600 | 1.1867974 | 1.1475325 | 1.1072304 | 1.0658597 | 1.0233929 | 0.9798061 | 0.9350795 | 0.8891972 | 0.8421477 | 0.7939237 | 0.7445224 | 0.6939455 | 0.6421993 | 0.5892946 | 0.5352475 | 0.4800782 | 0.4238123 | 0.3664799 | 0.3081161 | 0.2487609 | 0.1884587 | 0.1272589 | 0.0652155 | 0.0024214 | -0.0608280 | -0.1241828 | -0.1873177 | -0.2499330 | -0.3117543 | -0.3725318 | -0.4320397 | -0.4900756 | -0.5464589 | -0.6010295 | -0.6536466 | -0.7041869 | -0.7525429 | -0.7986214 | -0.8423413 | -0.8836323 | -0.9224328 | -0.9586879 | -0.9923479 | -1.0233666 | -1.0516988 | -1.0772992 | -1.1001200 | -1.1201094 | -1.1372094 | -1.1513538 | -1.1624659 | -1.1704568 | -1.1752223 | -1.1766420 | -1.1746795 | -1.1694344 | -1.1610003 | -1.1494529 | -1.1348525 | -1.1172460 | -1.0966683 | -1.0731446 | -1.0466911 | -1.0173172 | -0.9850268 | -0.9498193 | -0.9116918 | -0.8706398 | -0.8266590 | -0.7797468 | -0.7299038 | -0.6771350 | -0.6214522 | -0.5628749 | -0.5014321 | -0.4371647 | -0.3701263 | -0.3003857 | -0.2280283 | -0.1531580 | -0.0758991 |
| Insm1 | 1.8643682 | 1.8355346 | 1.8067934 | 1.7780040 | 1.7490302 | 1.7197411 | 1.6900102 | 1.6597164 | 1.6287440 | 1.5969824 | 1.5643274 | 1.5306805 | 1.4959498 | 1.4600504 | 1.422905 | 1.384442 | 1.344601 | 1.3033282 | 1.2605787 | 1.2163173 | 1.1705185 | 1.1231668 | 1.0742570 | 1.0237948 | 0.9717964 | 0.9182895 | 0.8633126 | 0.8069157 | 0.7491599 | 0.6901172 | 0.6298707 | 0.5685137 | 0.5061501 | 0.4428929 | 0.3788644 | 0.3141952 | 0.2490232 | 0.1834930 | 0.1177549 | 0.0519634 | -0.0137232 | -0.0791450 | -0.1441014 | -0.2081775 | -0.2709335 | -0.3319968 | -0.3910596 | -0.4478747 | -0.5022506 | -0.5540467 | -0.6031673 | -0.6495564 | -0.6931917 | -0.7340795 | -0.7722497 | -0.8077510 | -0.8406461 | -0.8710084 | -0.8989181 | -0.9244588 | -0.9477153 | -0.9687702 | -0.9877027 | -1.0045855 | -1.0194838 | -1.0324534 | -1.0435387 | -1.0527711 | -1.0601677 | -1.0657288 | -1.0694356 | -1.0712482 | -1.0711029 | -1.0689695 | -1.0648829 | -1.0588589 | -1.0508894 | -1.0409437 | -1.0289698 | -1.0148954 | -0.9986286 | -0.9800582 | -0.9590542 | -0.9354676 | -0.9091311 | -0.8798591 | -0.8474479 | -0.8116762 | -0.7723056 | -0.7290820 | -0.6817364 | -0.6299868 | -0.5735408 | -0.5120980 | -0.4453540 | -0.3730047 | -0.2947517 | -0.2103081 | -0.1194066 | -0.0218068 |
| Lhx9 | 1.9369366 | 1.9005958 | 1.8645245 | 1.8286014 | 1.7927107 | 1.7567416 | 1.7205887 | 1.6841519 | 1.6473364 | 1.6100531 | 1.5722184 | 1.5337545 | 1.4945895 | 1.4546580 | 1.413901 | 1.372264 | 1.329704 | 1.2861800 | 1.2416610 | 1.1961226 | 1.1495481 | 1.1019286 | 1.0532629 | 1.0035579 | 0.9528286 | 0.9010979 | 0.8483970 | 0.7947648 | 0.7402484 | 0.6849025 | 0.6287895 | 0.5719788 | 0.5145470 | 0.4565770 | 0.3981582 | 0.3393852 | 0.2803579 | 0.2211806 | 0.1619613 | 0.1028111 | 0.0438437 | -0.0148261 | -0.0730528 | -0.1305280 | -0.1869214 | -0.2419497 | -0.2953752 | -0.3470029 | -0.3966775 | -0.4442802 | -0.4897253 | -0.5329559 | -0.5739414 | -0.6126729 | -0.6491607 | -0.6834306 | -0.7155211 | -0.7454808 | -0.7733655 | -0.7992365 | -0.8231582 | -0.8451963 | -0.8654162 | -0.8838819 | -0.9006542 | -0.9157898 | -0.9293403 | -0.9413510 | -0.9518603 | -0.9608983 | -0.9684860 | -0.9746345 | -0.9793444 | -0.9826463 | -0.9846213 | -0.9853402 | -0.9848604 | -0.9832272 | -0.9804761 | -0.9766333 | -0.9717173 | -0.9657397 | -0.9587066 | -0.9506187 | -0.9414726 | -0.9312616 | -0.9199759 | -0.9076040 | -0.8941331 | -0.8795499 | -0.8638414 | -0.8469960 | -0.8290040 | -0.8098592 | -0.7895591 | -0.7681067 | -0.7455114 | -0.7217902 | -0.6969688 | -0.6710834 |
| Dlx5 | 1.7527835 | 1.7262526 | 1.6998093 | 1.6733763 | 1.6468783 | 1.6202419 | 1.5933958 | 1.5662706 | 1.5387991 | 1.5109161 | 1.4825587 | 1.4536663 | 1.4241805 | 1.3940454 | 1.363208 | 1.331617 | 1.299226 | 1.2659882 | 1.2318630 | 1.1968113 | 1.1607976 | 1.1237900 | 1.0857600 | 1.0466828 | 1.0065373 | 0.9653067 | 0.9229777 | 0.8795417 | 0.8349939 | 0.7893342 | 0.7425666 | 0.6946998 | 0.6457470 | 0.5957259 | 0.5446590 | 0.4925731 | 0.4394998 | 0.3854752 | 0.3305398 | 0.2747386 | 0.2181209 | 0.1607401 | 0.1026822 | 0.0441997 | -0.0144107 | -0.0728739 | -0.1309360 | -0.1883650 | -0.2449500 | -0.3005008 | -0.3548469 | -0.4078369 | -0.4593371 | -0.5092307 | -0.5574163 | -0.6038067 | -0.6483277 | -0.6909162 | -0.7315197 | -0.7700943 | -0.8066035 | -0.8410169 | -0.8733090 | -0.9034578 | -0.9314434 | -0.9572471 | -0.9808499 | -1.0022312 | -1.0213678 | -1.0382325 | -1.0527929 | -1.0650098 | -1.0748375 | -1.0822938 | -1.0874956 | -1.0905553 | -1.0915734 | -1.0906396 | -1.0878346 | -1.0832315 | -1.0768961 | -1.0688891 | -1.0592663 | -1.0480796 | -1.0353784 | -1.0212097 | -1.0056195 | -0.9886532 | -0.9703565 | -0.9507761 | -0.9299603 | -0.9079596 | -0.8848278 | -0.8606222 | -0.8354042 | -0.8092402 | -0.7822022 | -0.7543680 | -0.7258217 | -0.6966549 |
| Csde1 | 2.2817896 | 2.2117013 | 2.1419152 | 2.0724399 | 2.0032836 | 1.9344543 | 1.8659599 | 1.7978083 | 1.7300071 | 1.6625637 | 1.5954855 | 1.5287796 | 1.4624530 | 1.3965126 | 1.330965 | 1.265817 | 1.201075 | 1.1367448 | 1.0728330 | 1.0093454 | 0.9462879 | 0.8836661 | 0.8214855 | 0.7597516 | 0.6984695 | 0.6376445 | 0.5772814 | 0.5173851 | 0.4579603 | 0.3990115 | 0.3405433 | 0.2825598 | 0.2250652 | 0.1680637 | 0.1115591 | 0.0555552 | 0.0000557 | -0.0549359 | -0.1094162 | -0.1633817 | -0.2168294 | -0.2697560 | -0.3221454 | -0.3739025 | -0.4249052 | -0.4750336 | -0.5241698 | -0.5721981 | -0.6190046 | -0.6644774 | -0.7085062 | -0.7509823 | -0.7917986 | -0.8308489 | -0.8680285 | -0.9032331 | -0.9363595 | -0.9673048 | -0.9959661 | -1.0222409 | -1.0460260 | -1.0672179 | -1.0857121 | -1.1014030 | -1.1141836 | -1.1239450 | -1.1305763 | -1.1339639 | -1.1339914 | -1.1305394 | -1.1234845 | -1.1126994 | -1.0980541 | -1.0795124 | -1.0571850 | -1.0311922 | -1.0016518 | -0.9686794 | -0.9323894 | -0.8928951 | -0.8503089 | -0.8047433 | -0.7563106 | -0.7051240 | -0.6512973 | -0.5949458 | -0.5361861 | -0.4751369 | -0.4119188 | -0.3466550 | -0.2794712 | -0.2104962 | -0.1398615 | -0.0677022 | 0.0058432 | 0.0806328 | 0.1565208 | 0.2333578 | 0.3109903 | 0.3892609 |
| Ybx1 | 2.2541043 | 2.1892731 | 2.1245399 | 2.0599165 | 1.9954142 | 1.9310444 | 1.8668185 | 1.8027479 | 1.7388437 | 1.6751172 | 1.6115795 | 1.5482418 | 1.4851149 | 1.4222100 | 1.359538 | 1.297109 | 1.234935 | 1.1730258 | 1.1113922 | 1.0500449 | 0.9889941 | 0.9282504 | 0.8678239 | 0.8077250 | 0.7479637 | 0.6885501 | 0.6294941 | 0.5708056 | 0.5124944 | 0.4545701 | 0.3970423 | 0.3399205 | 0.2832141 | 0.2269324 | 0.1710846 | 0.1156797 | 0.0607268 | 0.0062347 | -0.0477878 | -0.1013319 | -0.1543892 | -0.2069511 | -0.2589984 | -0.3104478 | -0.3611929 | -0.4111284 | -0.4601497 | -0.5081532 | -0.5550362 | -0.6006969 | -0.6450340 | -0.6879474 | -0.7293374 | -0.7691050 | -0.8071521 | -0.8433806 | -0.8776932 | -0.9099928 | -0.9401825 | -0.9681657 | -0.9938457 | -1.0171256 | -1.0379084 | -1.0560965 | -1.0715922 | -1.0842966 | -1.0941104 | -1.1009331 | -1.1046629 | -1.1051971 | -1.1024310 | -1.0962585 | -1.0865733 | -1.0733552 | -1.0567173 | -1.0367823 | -1.0136721 | -0.9875077 | -0.9584095 | -0.9264974 | -0.8918912 | -0.8547108 | -0.8150759 | -0.7731070 | -0.7289247 | -0.6826505 | -0.6344065 | -0.5843158 | -0.5325024 | -0.4790912 | -0.4242085 | -0.3679816 | -0.3105392 | -0.2520111 | -0.1925285 | -0.1322239 | -0.0712311 | -0.0096854 | 0.0522770 | 0.1145181 |
| Zfp326 | 2.1999240 | 2.1373143 | 2.0750584 | 2.0131481 | 1.9515749 | 1.8903308 | 1.8294079 | 1.7687982 | 1.7084943 | 1.6484887 | 1.5887740 | 1.5293431 | 1.4701890 | 1.4113050 | 1.352684 | 1.294320 | 1.236207 | 1.1783378 | 1.1207069 | 1.0633084 | 1.0061365 | 0.9491856 | 0.8924504 | 0.8359255 | 0.7796058 | 0.7234864 | 0.6675623 | 0.6118290 | 0.5562820 | 0.5009168 | 0.4457292 | 0.3907152 | 0.3358708 | 0.2811922 | 0.2266758 | 0.1723181 | 0.1181157 | 0.0640655 | 0.0101644 | -0.0435906 | -0.0972021 | -0.1506729 | -0.2039885 | -0.2570351 | -0.3096656 | -0.3617372 | -0.4131113 | -0.4636533 | -0.5132325 | -0.5617224 | -0.6089997 | -0.6549447 | -0.6994409 | -0.7423748 | -0.7836354 | -0.8231144 | -0.8607051 | -0.8963029 | -0.9298042 | -0.9611067 | -0.9901084 | -1.0167075 | -1.0408020 | -1.0622889 | -1.0810640 | -1.0970214 | -1.1100527 | -1.1200467 | -1.1268887 | -1.1304596 | -1.1306359 | -1.1272884 | -1.1202834 | -1.1095805 | -1.0952849 | -1.0775096 | -1.0563633 | -1.0319507 | -1.0043738 | -0.9737320 | -0.9401229 | -0.9036431 | -0.8643884 | -0.8224547 | -0.7779382 | -0.7309363 | -0.6815477 | -0.6298730 | -0.5760152 | -0.5200802 | -0.4621769 | -0.4024179 | -0.3409196 | -0.2778028 | -0.2131928 | -0.1472196 | -0.0800186 | -0.0117302 | 0.0574996 | 0.1275189 |
| Zfp367 | 2.8042133 | 2.6739274 | 2.5471048 | 2.4236881 | 2.3036189 | 2.1868376 | 2.0732839 | 1.9628966 | 1.8556140 | 1.7513739 | 1.6501138 | 1.5517710 | 1.4562824 | 1.3635852 | 1.273617 | 1.186314 | 1.101614 | 1.0194561 | 0.9397776 | 0.8625175 | 0.7876152 | 0.7150108 | 0.6446448 | 0.5764587 | 0.5103947 | 0.4463957 | 0.3844057 | 0.3243694 | 0.2662324 | 0.2099415 | 0.1554442 | 0.1026892 | 0.0516261 | 0.0022056 | -0.0456207 | -0.0918999 | -0.1366783 | -0.1800010 | -0.2219120 | -0.2624545 | -0.3016703 | -0.3396004 | -0.3762766 | -0.4116845 | -0.4457980 | -0.4785971 | -0.5100671 | -0.5401985 | -0.5689859 | -0.5964273 | -0.6225242 | -0.6472803 | -0.6707012 | -0.6927942 | -0.7135671 | -0.7330286 | -0.7511869 | -0.7680501 | -0.7836251 | -0.7979174 | -0.8109309 | -0.8226669 | -0.8331245 | -0.8422992 | -0.8501830 | -0.8567640 | -0.8620255 | -0.8659456 | -0.8684967 | -0.8696446 | -0.8693481 | -0.8675577 | -0.8642159 | -0.8592948 | -0.8528183 | -0.8448074 | -0.8352765 | -0.8242341 | -0.8116830 | -0.7976217 | -0.7820444 | -0.7649418 | -0.7463016 | -0.7261096 | -0.7043495 | -0.6810040 | -0.6560553 | -0.6294859 | -0.6012790 | -0.5714195 | -0.5398943 | -0.5066938 | -0.4718121 | -0.4352480 | -0.3970061 | -0.3570975 | -0.3155410 | -0.2723638 | -0.2276027 | -0.1813050 |
| Dlx2 | 2.4816524 | 2.3908621 | 2.3014926 | 2.2135248 | 2.1269398 | 2.0417189 | 1.9578435 | 1.8752951 | 1.7940557 | 1.7141072 | 1.6354318 | 1.5580121 | 1.4818305 | 1.4068699 | 1.333113 | 1.260544 | 1.189145 | 1.1188998 | 1.0497928 | 0.9818076 | 0.9149284 | 0.8491396 | 0.7844255 | 0.7207711 | 0.6581611 | 0.5965807 | 0.5360151 | 0.4764498 | 0.4178705 | 0.3602629 | 0.3036131 | 0.2479073 | 0.1931317 | 0.1392731 | 0.0863180 | 0.0342533 | -0.0169339 | -0.0672564 | -0.1167268 | -0.1653575 | -0.2131609 | -0.2601490 | -0.3063204 | -0.3515959 | -0.3958748 | -0.4390650 | -0.4810823 | -0.5218504 | -0.5612998 | -0.5993679 | -0.6359978 | -0.6711379 | -0.7047415 | -0.7367661 | -0.7671724 | -0.7959243 | -0.8229877 | -0.8483301 | -0.8719200 | -0.8937261 | -0.9137167 | -0.9318589 | -0.9481182 | -0.9624576 | -0.9748365 | -0.9852107 | -0.9935310 | -0.9997424 | -1.0037835 | -1.0055852 | -1.0050697 | -1.0021496 | -0.9967276 | -0.9887612 | -0.9782995 | -0.9653906 | -0.9500748 | -0.9323850 | -0.9123482 | -0.8899863 | -0.8653166 | -0.8383532 | -0.8091075 | -0.7775893 | -0.7438074 | -0.7077704 | -0.6694879 | -0.6289709 | -0.5862328 | -0.5412906 | -0.4941652 | -0.4448829 | -0.3934757 | -0.3399828 | -0.2844510 | -0.2269359 | -0.1675029 | -0.1062278 | -0.0431979 | 0.0214874 |
| Hmgb1 | 2.5242832 | 2.4375062 | 2.3509347 | 2.2646157 | 2.1785956 | 2.0929208 | 2.0076374 | 1.9227912 | 1.8384277 | 1.7545920 | 1.6713290 | 1.5886830 | 1.5066980 | 1.4254174 | 1.344884 | 1.265141 | 1.186230 | 1.1081925 | 1.0310690 | 0.9548998 | 0.8797245 | 0.8055820 | 0.7325104 | 0.6605471 | 0.5897288 | 0.5200916 | 0.4516707 | 0.3845003 | 0.3186143 | 0.2540455 | 0.1908258 | 0.1289868 | 0.0685587 | 0.0095715 | -0.0479459 | -0.1039652 | -0.1584588 | -0.2113999 | -0.2627622 | -0.3125201 | -0.3606485 | -0.4071229 | -0.4519199 | -0.4950209 | -0.5364090 | -0.5760675 | -0.6139799 | -0.6501300 | -0.6845013 | -0.7170775 | -0.7478421 | -0.7767785 | -0.8038697 | -0.8290986 | -0.8524475 | -0.8738983 | -0.8934324 | -0.9110305 | -0.9266727 | -0.9403381 | -0.9520053 | -0.9616515 | -0.9692532 | -0.9747859 | -0.9782236 | -0.9795394 | -0.9787049 | -0.9756905 | -0.9704651 | -0.9629961 | -0.9532494 | -0.9411894 | -0.9267796 | -0.9100252 | -0.8909961 | -0.8697671 | -0.8464125 | -0.8210061 | -0.7936218 | -0.7643335 | -0.7332152 | -0.7003413 | -0.6657869 | -0.6296275 | -0.5919395 | -0.5528002 | -0.5122877 | -0.4704814 | -0.4274616 | -0.3833099 | -0.3381089 | -0.2919428 | -0.2448968 | -0.1970574 | -0.1485125 | -0.0993511 | -0.0496638 | 0.0004580 | 0.0509214 | 0.1016323 |
| Smarce1 | 2.5789943 | 2.4838825 | 2.3895926 | 2.2961622 | 2.2036278 | 2.1120244 | 2.0213854 | 1.9317431 | 1.8431283 | 1.7555706 | 1.6690981 | 1.5837378 | 1.4995153 | 1.4164550 | 1.334580 | 1.253913 | 1.174474 | 1.0962827 | 1.0193587 | 0.9437191 | 0.8693807 | 0.7963593 | 0.7246695 | 0.6543253 | 0.5853398 | 0.5177252 | 0.4514930 | 0.3866541 | 0.3232185 | 0.2611958 | 0.2005949 | 0.1414241 | 0.0836915 | 0.0274045 | -0.0274299 | -0.0808049 | -0.1327141 | -0.1831512 | -0.2321103 | -0.2795855 | -0.3255710 | -0.3700613 | -0.4130495 | -0.4545232 | -0.4944680 | -0.5328693 | -0.5697126 | -0.6049833 | -0.6386667 | -0.6707477 | -0.7012109 | -0.7300407 | -0.7572208 | -0.7827345 | -0.8065644 | -0.8286923 | -0.8490995 | -0.8677660 | -0.8846713 | -0.8997935 | -0.9131097 | -0.9245958 | -0.9342263 | -0.9419743 | -0.9478113 | -0.9517073 | -0.9536305 | -0.9535472 | -0.9514220 | -0.9472169 | -0.9408923 | -0.9324059 | -0.9217137 | -0.9088131 | -0.8937662 | -0.8766393 | -0.8574972 | -0.8364041 | -0.8134231 | -0.7886170 | -0.7620485 | -0.7337799 | -0.7038738 | -0.6723933 | -0.6394019 | -0.6049637 | -0.5691440 | -0.5320088 | -0.4936256 | -0.4540631 | -0.4133916 | -0.3716830 | -0.3290108 | -0.2854505 | -0.2410796 | -0.1959776 | -0.1502260 | -0.1039086 | -0.0571115 | -0.0099231 |
| Gabpb1 | 2.6514439 | 2.5421729 | 2.4350627 | 2.3301112 | 2.2273138 | 2.1266636 | 2.0281519 | 1.9317677 | 1.8374984 | 1.7453295 | 1.6552448 | 1.5672266 | 1.4812557 | 1.3973117 | 1.315373 | 1.235416 | 1.157417 | 1.0813507 | 1.0071920 | 0.9349138 | 0.8644889 | 0.7958893 | 0.7290864 | 0.6640514 | 0.6007549 | 0.5391673 | 0.4792587 | 0.4209990 | 0.3643582 | 0.3093059 | 0.2558120 | 0.2038464 | 0.1533790 | 0.1043799 | 0.0568194 | 0.0106682 | -0.0341029 | -0.0775227 | -0.1196197 | -0.1604220 | -0.1999573 | -0.2382526 | -0.2753321 | -0.3112037 | -0.3458701 | -0.3793354 | -0.4116043 | -0.4426823 | -0.4725755 | -0.5012903 | -0.5288337 | -0.5552126 | -0.5804341 | -0.6045052 | -0.6274325 | -0.6492227 | -0.6698816 | -0.6894147 | -0.7078269 | -0.7251220 | -0.7413032 | -0.7563726 | -0.7703309 | -0.7831779 | -0.7949119 | -0.8055296 | -0.8150261 | -0.8233948 | -0.8306271 | -0.8367124 | -0.8416378 | -0.8453882 | -0.8479461 | -0.8493181 | -0.8495480 | -0.8486803 | -0.8467571 | -0.8438180 | -0.8399011 | -0.8350426 | -0.8292775 | -0.8226399 | -0.8151629 | -0.8068790 | -0.7978206 | -0.7880197 | -0.7775084 | -0.7663192 | -0.7544848 | -0.7420388 | -0.7290155 | -0.7154499 | -0.7013784 | -0.6868386 | -0.6718693 | -0.6565109 | -0.6408055 | -0.6247968 | -0.6085304 | -0.5920536 |
| Cbfb | 2.6271505 | 2.5294749 | 2.4325852 | 2.3365352 | 2.2413772 | 2.1471617 | 2.0539374 | 1.9617513 | 1.8706487 | 1.7806732 | 1.6918666 | 1.6042694 | 1.5179201 | 1.4328559 | 1.349112 | 1.266723 | 1.185722 | 1.1061384 | 1.0280034 | 0.9513450 | 0.8761906 | 0.8025661 | 0.7304964 | 0.6600051 | 0.5911151 | 0.5238480 | 0.4582246 | 0.3942651 | 0.3319884 | 0.2714133 | 0.2125575 | 0.1554383 | 0.1000727 | 0.0464769 | -0.0053329 | -0.0553408 | -0.1035312 | -0.1498886 | -0.1943974 | -0.2370419 | -0.2778063 | -0.3166747 | -0.3536387 | -0.3887367 | -0.4220233 | -0.4535510 | -0.4833710 | -0.5115328 | -0.5380845 | -0.5630728 | -0.5865430 | -0.6085390 | -0.6291037 | -0.6482788 | -0.6661048 | -0.6826213 | -0.6978669 | -0.7118793 | -0.7246951 | -0.7363505 | -0.7468807 | -0.7563202 | -0.7647028 | -0.7720618 | -0.7784298 | -0.7838391 | -0.7883212 | -0.7919074 | -0.7946284 | -0.7965147 | -0.7975964 | -0.7979033 | -0.7974648 | -0.7963092 | -0.7944628 | -0.7919516 | -0.7888015 | -0.7850383 | -0.7806875 | -0.7757748 | -0.7703255 | -0.7643653 | -0.7579193 | -0.7510132 | -0.7436722 | -0.7359219 | -0.7277878 | -0.7192953 | -0.7104702 | -0.7013382 | -0.6919250 | -0.6822565 | -0.6723589 | -0.6622583 | -0.6519809 | -0.6415533 | -0.6310019 | -0.6203536 | -0.6096352 | -0.5988738 |
| Olig2 | 2.7250149 | 2.6099930 | 2.4970088 | 2.3860935 | 2.2772741 | 2.1705736 | 2.0660115 | 1.9636037 | 1.8633623 | 1.7652965 | 1.6694120 | 1.5757116 | 1.4841952 | 1.3948601 | 1.307701 | 1.222710 | 1.139876 | 1.0591893 | 0.9806340 | 0.9041948 | 0.8298542 | 0.7575932 | 0.6873917 | 0.6192281 | 0.5530799 | 0.4889237 | 0.4267354 | 0.3664900 | 0.3081623 | 0.2517264 | 0.1971564 | 0.1444259 | 0.0935089 | 0.0443789 | -0.0029900 | -0.0486237 | -0.0925476 | -0.1347870 | -0.1753663 | -0.2143094 | -0.2516398 | -0.2873799 | -0.3215548 | -0.3542077 | -0.3853869 | -0.4151384 | -0.4435060 | -0.4705312 | -0.4962535 | -0.5207105 | -0.5439377 | -0.5659690 | -0.5868362 | -0.6065697 | -0.6251981 | -0.6427482 | -0.6592457 | -0.6747144 | -0.6891769 | -0.7026543 | -0.7151664 | -0.7267315 | -0.7373670 | -0.7470887 | -0.7559114 | -0.7638486 | -0.7709129 | -0.7771155 | -0.7824667 | -0.7869757 | -0.7906505 | -0.7934984 | -0.7955256 | -0.7967476 | -0.7971942 | -0.7968958 | -0.7958820 | -0.7941814 | -0.7918223 | -0.7888323 | -0.7852387 | -0.7810685 | -0.7763482 | -0.7711045 | -0.7653636 | -0.7591519 | -0.7524959 | -0.7454220 | -0.7379568 | -0.7301272 | -0.7219602 | -0.7134833 | -0.7047241 | -0.6957109 | -0.6864722 | -0.6770370 | -0.6674347 | -0.6576954 | -0.6478497 | -0.6379285 |
| Hmgb3 | 2.7941326 | 2.6801905 | 2.5671995 | 2.4552525 | 2.3444403 | 2.2348508 | 2.1265690 | 2.0196770 | 1.9142539 | 1.8103754 | 1.7081140 | 1.6075385 | 1.5087146 | 1.4117040 | 1.316565 | 1.223353 | 1.132117 | 1.0429058 | 0.9557624 | 0.8707269 | 0.7878355 | 0.7071210 | 0.6286127 | 0.5523370 | 0.4783166 | 0.4065714 | 0.3371186 | 0.2699726 | 0.2051450 | 0.1426456 | 0.0824819 | 0.0246594 | -0.0308177 | -0.0839469 | -0.1347265 | -0.1831560 | -0.2292351 | -0.2729641 | -0.3143434 | -0.3533730 | -0.3900524 | -0.4243805 | -0.4563670 | -0.4860903 | -0.5136508 | -0.5391447 | -0.5626642 | -0.5842977 | -0.6041298 | -0.6222421 | -0.6387129 | -0.6536176 | -0.6670291 | -0.6790176 | -0.6896513 | -0.6989962 | -0.7071165 | -0.7140746 | -0.7199316 | -0.7247472 | -0.7285797 | -0.7314865 | -0.7335242 | -0.7347486 | -0.7352147 | -0.7349772 | -0.7340902 | -0.7326075 | -0.7305828 | -0.7280697 | -0.7251215 | -0.7217916 | -0.7181335 | -0.7141838 | -0.7099543 | -0.7054548 | -0.7006949 | -0.6956842 | -0.6904325 | -0.6849493 | -0.6792445 | -0.6733276 | -0.6672085 | -0.6608971 | -0.6544030 | -0.6477363 | -0.6409068 | -0.6339247 | -0.6267998 | -0.6195425 | -0.6121628 | -0.6046711 | -0.5970777 | -0.5893931 | -0.5816277 | -0.5737921 | -0.5658971 | -0.5579534 | -0.5499719 | -0.5419634 |
| E2f2 | 2.9465733 | 2.7918114 | 2.6426217 | 2.4988414 | 2.3603095 | 2.2268671 | 2.0983572 | 1.9746255 | 1.8555202 | 1.7408919 | 1.6305944 | 1.5244843 | 1.4224210 | 1.3242675 | 1.229889 | 1.139156 | 1.051939 | 0.9681155 | 0.8875632 | 0.8101646 | 0.7358055 | 0.6643746 | 0.5957641 | 0.5298693 | 0.4665890 | 0.4058248 | 0.3474818 | 0.2914679 | 0.2376943 | 0.1860749 | 0.1365268 | 0.0889698 | 0.0433266 | -0.0004774 | -0.0425141 | -0.0828528 | -0.1215603 | -0.1587008 | -0.1943362 | -0.2285261 | -0.2613276 | -0.2927959 | -0.3229810 | -0.3519151 | -0.3796248 | -0.4061374 | -0.4314810 | -0.4556838 | -0.4787741 | -0.5007803 | -0.5217304 | -0.5416523 | -0.5605730 | -0.5785192 | -0.5955167 | -0.6115904 | -0.6267642 | -0.6410610 | -0.6545026 | -0.6671093 | -0.6789005 | -0.6898938 | -0.7001056 | -0.7095506 | -0.7182420 | -0.7261913 | -0.7334081 | -0.7399002 | -0.7456735 | -0.7507319 | -0.7550770 | -0.7587081 | -0.7616226 | -0.7638312 | -0.7653666 | -0.7662604 | -0.7665414 | -0.7662362 | -0.7653693 | -0.7639633 | -0.7620394 | -0.7596177 | -0.7567169 | -0.7533552 | -0.7495502 | -0.7453188 | -0.7406778 | -0.7356442 | -0.7302348 | -0.7244668 | -0.7183577 | -0.7119258 | -0.7051900 | -0.6981701 | -0.6908868 | -0.6833620 | -0.6756189 | -0.6676818 | -0.6595768 | -0.6513311 |
| Zfp143 | 2.8759247 | 2.7403159 | 2.6079452 | 2.4788143 | 2.3529193 | 2.2302512 | 2.1107962 | 1.9945359 | 1.8814477 | 1.7715054 | 1.6646792 | 1.5609362 | 1.4602408 | 1.3625547 | 1.267837 | 1.176047 | 1.087139 | 1.0010687 | 0.9177888 | 0.8372523 | 0.7594109 | 0.6842159 | 0.6116184 | 0.5415694 | 0.4740199 | 0.4089210 | 0.3462245 | 0.2858825 | 0.2278478 | 0.1720742 | 0.1185161 | 0.0671293 | 0.0178703 | -0.0293026 | -0.0744302 | -0.1175518 | -0.1587049 | -0.1979257 | -0.2352486 | -0.2707062 | -0.3043293 | -0.3361469 | -0.3661926 | -0.3945366 | -0.4212593 | -0.4464365 | -0.4701396 | -0.4924362 | -0.5133899 | -0.5330611 | -0.5515068 | -0.5687812 | -0.5849355 | -0.6000187 | -0.6140770 | -0.6271546 | -0.6392938 | -0.6505347 | -0.6609159 | -0.6704742 | -0.6792451 | -0.6872625 | -0.6945592 | -0.7011669 | -0.7071160 | -0.7124362 | -0.7171562 | -0.7213038 | -0.7249062 | -0.7279901 | -0.7305813 | -0.7327053 | -0.7343870 | -0.7356480 | -0.7365050 | -0.7369741 | -0.7370710 | -0.7368113 | -0.7362104 | -0.7352835 | -0.7340456 | -0.7325117 | -0.7306965 | -0.7286150 | -0.7262818 | -0.7237117 | -0.7209193 | -0.7179193 | -0.7147265 | -0.7113557 | -0.7078216 | -0.7041393 | -0.7003236 | -0.6963898 | -0.6923528 | -0.6882281 | -0.6840311 | -0.6797772 | -0.6754823 | -0.6711620 |
| Zfp207 | 2.2646530 | 2.1978389 | 2.1312801 | 2.0649991 | 1.9990179 | 1.9333583 | 1.8680415 | 1.8030888 | 1.7385209 | 1.6743582 | 1.6106208 | 1.5473286 | 1.4845011 | 1.4221574 | 1.360316 | 1.298997 | 1.238217 | 1.1779947 | 1.1183477 | 1.0592934 | 1.0008489 | 0.9430312 | 0.8858568 | 0.8293421 | 0.7735030 | 0.7183555 | 0.6639150 | 0.6101970 | 0.5572165 | 0.5049884 | 0.4535273 | 0.4028478 | 0.3529640 | 0.3038901 | 0.2556400 | 0.2082273 | 0.1616655 | 0.1159682 | 0.0711486 | 0.0272198 | -0.0158053 | -0.0579137 | -0.0990936 | -0.1393396 | -0.1786485 | -0.2170171 | -0.2544422 | -0.2909204 | -0.3264484 | -0.3610228 | -0.3946400 | -0.4272967 | -0.4589890 | -0.4897134 | -0.5194661 | -0.5482430 | -0.5760403 | -0.6028539 | -0.6286795 | -0.6535128 | -0.6773493 | -0.7001845 | -0.7220135 | -0.7428315 | -0.7626335 | -0.7814141 | -0.7991681 | -0.8158899 | -0.8315737 | -0.8462137 | -0.8598035 | -0.8723371 | -0.8838080 | -0.8942279 | -0.9036356 | -0.9120718 | -0.9195771 | -0.9261916 | -0.9319552 | -0.9369075 | -0.9410879 | -0.9445357 | -0.9472900 | -0.9493896 | -0.9508734 | -0.9517801 | -0.9521482 | -0.9520162 | -0.9514226 | -0.9504058 | -0.9490042 | -0.9472562 | -0.9452000 | -0.9428740 | -0.9403166 | -0.9375662 | -0.9346611 | -0.9316398 | -0.9285406 | -0.9254022 |
| Zfp760 | 2.3256735 | 2.2488270 | 2.1727913 | 2.0975851 | 2.0232255 | 1.9497289 | 1.8771108 | 1.8053856 | 1.7345668 | 1.6646672 | 1.5956985 | 1.5276716 | 1.4605969 | 1.3944836 | 1.329340 | 1.265175 | 1.201995 | 1.1398074 | 1.0786172 | 1.0184302 | 0.9592511 | 0.9010842 | 0.8439331 | 0.7878011 | 0.7326910 | 0.6786050 | 0.6255450 | 0.5735126 | 0.5225090 | 0.4725349 | 0.4235910 | 0.3756776 | 0.3287946 | 0.2829419 | 0.2381191 | 0.1943256 | 0.1515607 | 0.1098237 | 0.0691136 | 0.0294294 | -0.0092300 | -0.0468654 | -0.0834810 | -0.1190975 | -0.1537414 | -0.1874383 | -0.2202132 | -0.2520902 | -0.2830928 | -0.3132437 | -0.3425651 | -0.3710785 | -0.3988048 | -0.4257642 | -0.4519765 | -0.4774609 | -0.5022359 | -0.5263199 | -0.5497303 | -0.5724845 | -0.5945991 | -0.6160904 | -0.6369744 | -0.6572665 | -0.6769818 | -0.6961350 | -0.7147405 | -0.7328123 | -0.7503640 | -0.7674090 | -0.7839604 | -0.8000308 | -0.8156328 | -0.8307814 | -0.8454955 | -0.8597938 | -0.8736949 | -0.8872170 | -0.9003779 | -0.9131952 | -0.9256863 | -0.9378682 | -0.9497576 | -0.9613711 | -0.9727250 | -0.9838353 | -0.9947180 | -1.0053886 | -1.0158628 | -1.0261557 | -1.0362825 | -1.0462581 | -1.0560973 | -1.0658147 | -1.0754247 | -1.0849417 | -1.0943798 | -1.1037529 | -1.1130751 | -1.1223599 |
write.table(heatmap_matrix_q_value_5_10_minus_5, file = file.path(tables_directory, "4-forebrain_astro_ependymal_joint_cortex_cluster_20_2_12_23-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)2.2.2.1.2 q value < 0.01
significant_genes_q_value_0.01 <- filter(diff_test_res_all_genes, qval < 0.01) %>% .$gene
cat("Number of significant genes: ", length(significant_genes_q_value_0.01))## Number of significant genes: 5880significant_transcription_factors_q_value_0.01 <- as.character(significant_genes_q_value_0.01[significant_genes_q_value_0.01 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_0.01))## Number of significant transcription factors: 296plot_genes_heatmap_output_q_value_0.01 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)
save_pheatmap_pdf(plot_genes_heatmap_output_q_value_0.01[[2]], file.path("figures", "4-forebrain_astro_ependymal_joint_cortex_cluster_20_2_12_23", "diff_test_plots_transcription_factors_only_q_value_0.01_heatmap_custom.pdf"), width=16, height=40)## pdf
## 2heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
ph_res_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[2]]
pheatmap_ordering_q_value_0.01 <- rownames(heatmap_matrix_q_value_0.01[ph_res_q_value_0.01$tree_row[["order"]],])
transcription_factors_table_q_value_0.01 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_0.01)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_0.01 <- transcription_factors_table_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))
write.table(transcription_factors_table_q_value_0.01, file.path(tables_directory, "4-forebrain_astro_ependymal_joint_cortex_cluster_20_2_12_23-significant_transcription_factors_diff_test_analysis_qval_0.01.txt"), sep="\t", quote=FALSE, row.names=FALSE)
heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
heatmap_matrix_q_value_0.01 <- as.data.frame(heatmap_matrix_q_value_0.01) %>% rownames_to_column("gene")
heatmap_matrix_q_value_0.01 <- heatmap_matrix_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))
heatmap_matrix_q_value_0.01 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")| gene | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Zeb1 | 1.925268 | 1.856328 | 1.787851 | 1.7199079 | 1.6525667 | 1.5858939 | 1.5199545 | 1.4548119 | 1.3905279 | 1.3271627 | 1.2647751 | 1.2034223 | 1.1431601 | 1.0840432 | 1.0261247 | 0.9694565 | 0.9140893 | 0.8600728 | 0.8074556 | 0.7562851 | 0.7066081 | 0.6584705 | 0.6119174 | 0.5669933 | 0.5237421 | 0.4822073 | 0.4424320 | 0.4044593 | 0.3683317 | 0.3340920 | 0.3017831 | 0.2714479 | 0.2431298 | 0.2168725 | 0.1927205 | 0.1707188 | 0.1509134 | 0.1333511 | 0.1180800 | 0.1051494 | 0.0946100 | 0.0865143 | 0.0808811 | 0.0775220 | 0.0761737 | 0.0765744 | 0.0784635 | 0.0815809 | 0.0856667 | 0.0904611 | 0.0957038 | 0.1011339 | 0.1064902 | 0.1115105 | 0.1159323 | 0.1194925 | 0.1219280 | 0.1229756 | 0.1223725 | 0.1198572 | 0.1151690 | 0.1080497 | 0.0982437 | 0.0854986 | 0.0695666 | 0.0502048 | 0.0271766 | 0.0002525 | -0.0307887 | -0.0661587 | -0.1060587 | -0.1506778 | -0.2001888 | -0.2545838 | -0.3135924 | -0.3769195 | -0.4442677 | -0.5153392 | -0.5898360 | -0.6674618 | -0.7479227 | -0.8309280 | -0.9161914 | -1.0034318 | -1.0923740 | -1.1827493 | -1.274296 | -1.366762 | -1.459902 | -1.553479 | -1.647268 | -1.741051 | -1.834622 | -1.927783 | -2.020348 | -2.112141 | -2.202996 | -2.292757 | -2.381280 | -2.468428 |
| Nfib | 1.580629 | 1.546102 | 1.511625 | 1.4772113 | 1.4428718 | 1.4086190 | 1.3744648 | 1.3404211 | 1.3064998 | 1.2727127 | 1.2390714 | 1.2055878 | 1.1722735 | 1.1391400 | 1.1061989 | 1.0734617 | 1.0409398 | 1.0086445 | 0.9765871 | 0.9447790 | 0.9132314 | 0.8819553 | 0.8509619 | 0.8202623 | 0.7898674 | 0.7597883 | 0.7300358 | 0.7006207 | 0.6715540 | 0.6428464 | 0.6145085 | 0.5865512 | 0.5589850 | 0.5318205 | 0.5050684 | 0.4787391 | 0.4528432 | 0.4273911 | 0.4023932 | 0.3778600 | 0.3538019 | 0.3302291 | 0.3071418 | 0.2844795 | 0.2621597 | 0.2400998 | 0.2182180 | 0.1964324 | 0.1746616 | 0.1528243 | 0.1308396 | 0.1086270 | 0.0861061 | 0.0631968 | 0.0398195 | 0.0158949 | -0.0086561 | -0.0339120 | -0.0599511 | -0.0868511 | -0.1146894 | -0.1435427 | -0.1734873 | -0.2045988 | -0.2369524 | -0.2706225 | -0.3056826 | -0.3422058 | -0.3802640 | -0.4199285 | -0.4612693 | -0.5043558 | -0.5492550 | -0.5959767 | -0.6444445 | -0.6945750 | -0.7462849 | -0.7994910 | -0.8541104 | -0.9100604 | -0.9672587 | -1.0256234 | -1.0850730 | -1.1455264 | -1.2069031 | -1.2691233 | -1.332108 | -1.395777 | -1.460055 | -1.524863 | -1.590124 | -1.655764 | -1.721707 | -1.787881 | -1.854210 | -1.920625 | -1.987053 | -2.053424 | -2.119669 | -2.185721 |
| Tead2 | 1.816708 | 1.759707 | 1.703103 | 1.6469411 | 1.5912653 | 1.5361191 | 1.4815444 | 1.4275821 | 1.3742720 | 1.3216528 | 1.2697622 | 1.2186370 | 1.1683128 | 1.1188244 | 1.0702056 | 1.0224895 | 0.9757083 | 0.9298932 | 0.8850750 | 0.8412836 | 0.7985483 | 0.7568978 | 0.7163601 | 0.6769629 | 0.6387335 | 0.6016985 | 0.5658844 | 0.5313174 | 0.4980233 | 0.4660280 | 0.4353570 | 0.4060361 | 0.3780908 | 0.3515469 | 0.3264302 | 0.3027669 | 0.2805833 | 0.2599062 | 0.2407628 | 0.2231809 | 0.2071887 | 0.1928152 | 0.1800648 | 0.1687911 | 0.1587940 | 0.1498752 | 0.1418380 | 0.1344869 | 0.1276275 | 0.1210662 | 0.1146103 | 0.1080677 | 0.1012473 | 0.0939585 | 0.0860117 | 0.0772182 | 0.0673909 | 0.0563438 | 0.0438930 | 0.0298567 | 0.0140556 | -0.0036864 | -0.0235419 | -0.0456793 | -0.0702625 | -0.0974498 | -0.1273936 | -0.1602396 | -0.1961258 | -0.2351822 | -0.2775296 | -0.3232788 | -0.3725281 | -0.4252440 | -0.4812046 | -0.5401715 | -0.6019070 | -0.6661746 | -0.7327401 | -0.8013723 | -0.8718437 | -0.9439314 | -1.0174174 | -1.0920895 | -1.1677415 | -1.2441739 | -1.321194 | -1.398617 | -1.476266 | -1.553969 | -1.631567 | -1.708904 | -1.785836 | -1.862226 | -1.937944 | -2.012870 | -2.086890 | -2.159900 | -2.231803 | -2.302509 |
| Hif1a | 1.681940 | 1.635538 | 1.589295 | 1.5432478 | 1.4974292 | 1.4518730 | 1.4066126 | 1.3616811 | 1.3171110 | 1.2729346 | 1.2291839 | 1.1858904 | 1.1430854 | 1.1007998 | 1.0590642 | 1.0179090 | 0.9773641 | 0.9374593 | 0.8982241 | 0.8596877 | 0.8218790 | 0.7848269 | 0.7485598 | 0.7131060 | 0.6784936 | 0.6447508 | 0.6119052 | 0.5799845 | 0.5490163 | 0.5190280 | 0.4900471 | 0.4621008 | 0.4352165 | 0.4094213 | 0.3847425 | 0.3612074 | 0.3388433 | 0.3176776 | 0.2977378 | 0.2790514 | 0.2616463 | 0.2455502 | 0.2307701 | 0.2171866 | 0.2046346 | 0.1929497 | 0.1819683 | 0.1715270 | 0.1614634 | 0.1516153 | 0.1418208 | 0.1319189 | 0.1217484 | 0.1111491 | 0.0999611 | 0.0880248 | 0.0751815 | 0.0612731 | 0.0461423 | 0.0296329 | 0.0115894 | -0.0081422 | -0.0297146 | -0.0532788 | -0.0789842 | -0.1069780 | -0.1374052 | -0.1704086 | -0.2061278 | -0.2446997 | -0.2862576 | -0.3309315 | -0.3788453 | -0.4300131 | -0.4842857 | -0.5414999 | -0.6014928 | -0.6641016 | -0.7291643 | -0.7965197 | -0.8660077 | -0.9374697 | -1.0107485 | -1.0856889 | -1.1621374 | -1.2399430 | -1.318957 | -1.399032 | -1.480025 | -1.561795 | -1.644203 | -1.727114 | -1.810395 | -1.893916 | -1.977552 | -2.061179 | -2.144677 | -2.227929 | -2.310820 | -2.393240 |
| Olig1 | 1.597122 | 1.554088 | 1.511201 | 1.4684945 | 1.4260030 | 1.3837594 | 1.3417965 | 1.3001470 | 1.2588429 | 1.2179160 | 1.1773979 | 1.1373195 | 1.0977117 | 1.0586047 | 1.0200287 | 0.9820133 | 0.9445880 | 0.9077818 | 0.8716233 | 0.8361412 | 0.8013636 | 0.7673184 | 0.7340332 | 0.7015354 | 0.6698522 | 0.6390106 | 0.6090374 | 0.5799591 | 0.5518023 | 0.5245931 | 0.4983580 | 0.4731228 | 0.4489138 | 0.4257569 | 0.4036782 | 0.3827036 | 0.3628592 | 0.3441712 | 0.3266656 | 0.3103690 | 0.2953078 | 0.2815086 | 0.2689760 | 0.2575814 | 0.2471479 | 0.2374995 | 0.2284607 | 0.2198569 | 0.2115138 | 0.2032578 | 0.1949155 | 0.1863143 | 0.1772819 | 0.1676466 | 0.1572375 | 0.1458841 | 0.1334170 | 0.1196678 | 0.1044691 | 0.0876552 | 0.0690618 | 0.0485266 | 0.0258892 | 0.0009921 | -0.0263198 | -0.0561981 | -0.0887910 | -0.1242427 | -0.1626929 | -0.2042762 | -0.2491220 | -0.2973535 | -0.3490852 | -0.4043110 | -0.4628471 | -0.5244942 | -0.5890522 | -0.6563209 | -0.7261004 | -0.7981915 | -0.8723962 | -0.9485180 | -1.0263622 | -1.1057367 | -1.1864519 | -1.2683214 | -1.351162 | -1.434795 | -1.519045 | -1.603741 | -1.688717 | -1.773812 | -1.858871 | -1.943741 | -2.028279 | -2.112345 | -2.195806 | -2.278534 | -2.360407 | -2.441312 |
| Foxg1 | 1.617490 | 1.557250 | 1.497304 | 1.4377294 | 1.3786018 | 1.3199960 | 1.2619855 | 1.2046429 | 1.1480397 | 1.0922463 | 1.0373323 | 0.9833662 | 0.9304156 | 0.8785473 | 0.8278273 | 0.7783207 | 0.7300920 | 0.6832049 | 0.6377227 | 0.5937079 | 0.5512226 | 0.5103287 | 0.4710874 | 0.4335599 | 0.3978070 | 0.3638895 | 0.3318682 | 0.3018038 | 0.2737572 | 0.2477897 | 0.2239626 | 0.2023380 | 0.1829782 | 0.1659463 | 0.1513061 | 0.1391223 | 0.1294606 | 0.1223876 | 0.1179713 | 0.1162810 | 0.1173875 | 0.1213631 | 0.1282379 | 0.1377814 | 0.1496675 | 0.1635700 | 0.1791624 | 0.1961176 | 0.2141070 | 0.2328012 | 0.2518687 | 0.2709767 | 0.2897905 | 0.3079738 | 0.3251886 | 0.3410956 | 0.3553543 | 0.3676234 | 0.3775613 | 0.3848263 | 0.3890777 | 0.3899759 | 0.3871832 | 0.3803650 | 0.3691903 | 0.3533326 | 0.3324714 | 0.3062925 | 0.2744898 | 0.2367665 | 0.1928358 | 0.1424229 | 0.0852699 | 0.0213537 | -0.0490028 | -0.1254440 | -0.2076116 | -0.2951454 | -0.3876847 | -0.4848695 | -0.5863412 | -0.6917440 | -0.8007258 | -0.9129388 | -1.0280404 | -1.1456943 | -1.265571 | -1.387347 | -1.510709 | -1.635350 | -1.760974 | -1.887291 | -2.014024 | -2.140903 | -2.267671 | -2.394077 | -2.519884 | -2.644862 | -2.768795 | -2.891473 |
| Zmiz1 | 1.692460 | 1.620128 | 1.548284 | 1.4770258 | 1.4064517 | 1.3366561 | 1.2677317 | 1.1997693 | 1.1328575 | 1.0670831 | 1.0025311 | 0.9392846 | 0.8774250 | 0.8170324 | 0.7581850 | 0.7009598 | 0.6454326 | 0.5916778 | 0.5397690 | 0.4897787 | 0.4417787 | 0.3958401 | 0.3520335 | 0.3104293 | 0.2710975 | 0.2341082 | 0.1995316 | 0.1674381 | 0.1378988 | 0.1109854 | 0.0867703 | 0.0653274 | 0.0467314 | 0.0310587 | 0.0183876 | 0.0087980 | 0.0023723 | -0.0008049 | -0.0006463 | 0.0029386 | 0.0100432 | 0.0207646 | 0.0351502 | 0.0529327 | 0.0737289 | 0.0971551 | 0.1228261 | 0.1503547 | 0.1793509 | 0.2094211 | 0.2401680 | 0.2711898 | 0.3020808 | 0.3324305 | 0.3618246 | 0.3898446 | 0.4160685 | 0.4400715 | 0.4614265 | 0.4797050 | 0.4944783 | 0.5053183 | 0.5117993 | 0.5134992 | 0.5100009 | 0.5008944 | 0.4857787 | 0.4642634 | 0.4359712 | 0.4005401 | 0.3576257 | 0.3069037 | 0.2480769 | 0.1811419 | 0.1065214 | 0.0246817 | -0.0639050 | -0.1587625 | -0.2594134 | -0.3653805 | -0.4761893 | -0.5913699 | -0.7104583 | -0.8329983 | -0.9585432 | -1.0866568 | -1.216915 | -1.348906 | -1.482232 | -1.616511 | -1.751375 | -1.886472 | -2.021469 | -2.156045 | -2.289901 | -2.422751 | -2.554328 | -2.684380 | -2.812675 | -2.938994 |
| Sox8 | 1.541021 | 1.472372 | 1.404425 | 1.3372801 | 1.2710316 | 1.2057720 | 1.1415897 | 1.0785697 | 1.0167939 | 0.9563410 | 0.8972867 | 0.8397039 | 0.7836630 | 0.7292316 | 0.6764755 | 0.6254579 | 0.5762404 | 0.5288829 | 0.4834439 | 0.4399806 | 0.3985491 | 0.3592051 | 0.3220035 | 0.2869992 | 0.2542470 | 0.2238021 | 0.1957205 | 0.1700588 | 0.1468751 | 0.1262289 | 0.1081817 | 0.0927970 | 0.0801412 | 0.0702833 | 0.0632959 | 0.0592551 | 0.0582413 | 0.0603393 | 0.0656390 | 0.0742358 | 0.0862311 | 0.1017327 | 0.1207991 | 0.1431576 | 0.1684119 | 0.1961630 | 0.2260070 | 0.2575338 | 0.2903259 | 0.3239571 | 0.3579922 | 0.3919862 | 0.4254844 | 0.4580226 | 0.4891280 | 0.5183194 | 0.5451092 | 0.5690045 | 0.5895093 | 0.6061268 | 0.6183617 | 0.6257239 | 0.6277310 | 0.6239125 | 0.6138136 | 0.5969993 | 0.5730590 | 0.5416113 | 0.5023089 | 0.4548433 | 0.3989504 | 0.3344155 | 0.2610836 | 0.1791532 | 0.0893108 | -0.0077041 | -0.1111443 | -0.2202614 | -0.3343119 | -0.4525625 | -0.5742961 | -0.6988159 | -0.8254499 | -0.9535550 | -1.0825199 | -1.2117682 | -1.340760 | -1.468995 | -1.596013 | -1.721391 | -1.844752 | -1.965755 | -2.084102 | -2.199533 | -2.311824 | -2.420790 | -2.526278 | -2.628168 | -2.726370 | -2.820821 |
| Tcf4 | 1.188263 | 1.164544 | 1.140864 | 1.1172416 | 1.0936946 | 1.0702412 | 1.0468995 | 1.0236873 | 1.0006227 | 0.9777234 | 0.9550072 | 0.9324920 | 0.9101952 | 0.8881346 | 0.8663276 | 0.8447917 | 0.8235445 | 0.8026031 | 0.7819850 | 0.7617073 | 0.7417874 | 0.7222424 | 0.7030893 | 0.6843453 | 0.6660275 | 0.6481527 | 0.6307380 | 0.6138004 | 0.5973566 | 0.5814237 | 0.5660184 | 0.5511576 | 0.5368582 | 0.5231369 | 0.5100106 | 0.4974962 | 0.4856103 | 0.4743700 | 0.4637920 | 0.4538932 | 0.4446905 | 0.4362008 | 0.4284214 | 0.4212326 | 0.4144716 | 0.4079761 | 0.4015836 | 0.3951321 | 0.3884596 | 0.3814043 | 0.3738047 | 0.3654995 | 0.3563278 | 0.3461287 | 0.3347421 | 0.3220082 | 0.3077678 | 0.2918625 | 0.2741345 | 0.2544272 | 0.2325847 | 0.2084528 | 0.1818784 | 0.1527100 | 0.1207979 | 0.0859946 | 0.0481545 | 0.0071349 | -0.0372045 | -0.0850009 | -0.1363878 | -0.1914954 | -0.2504476 | -0.3132493 | -0.3797277 | -0.4496947 | -0.5229614 | -0.5993386 | -0.6786371 | -0.7606679 | -0.8452423 | -0.9321722 | -1.0212704 | -1.1123509 | -1.2052288 | -1.2997211 | -1.395646 | -1.492825 | -1.591080 | -1.690236 | -1.790122 | -1.890568 | -1.991408 | -2.092480 | -2.193623 | -2.294682 | -2.395504 | -2.495942 | -2.595851 | -2.695092 |
| Emx2 | 1.388616 | 1.350363 | 1.312306 | 1.2744825 | 1.2369310 | 1.1996891 | 1.1627933 | 1.1262800 | 1.0901847 | 1.0545424 | 1.0193875 | 0.9847538 | 0.9506748 | 0.9171833 | 0.8843115 | 0.8520914 | 0.8205544 | 0.7897314 | 0.7596531 | 0.7303498 | 0.7018514 | 0.6741875 | 0.6473874 | 0.6214804 | 0.5964952 | 0.5724607 | 0.5494055 | 0.5273582 | 0.5063472 | 0.4864011 | 0.4675484 | 0.4498177 | 0.4332378 | 0.4178375 | 0.4036461 | 0.3906929 | 0.3790077 | 0.3686206 | 0.3595622 | 0.3518634 | 0.3455559 | 0.3406718 | 0.3372148 | 0.3350157 | 0.3338426 | 0.3334637 | 0.3336478 | 0.3341639 | 0.3347806 | 0.3352670 | 0.3353917 | 0.3349235 | 0.3336313 | 0.3312846 | 0.3276532 | 0.3225081 | 0.3156215 | 0.3067677 | 0.2957233 | 0.2822676 | 0.2661841 | 0.2472602 | 0.2252888 | 0.2000685 | 0.1714050 | 0.1391118 | 0.1030112 | 0.0629352 | 0.0187268 | -0.0297589 | -0.0826539 | -0.1400758 | -0.2021244 | -0.2687321 | -0.3395926 | -0.4143788 | -0.4927640 | -0.5744236 | -0.6590361 | -0.7462841 | -0.8358563 | -0.9274474 | -1.0207603 | -1.1155057 | -1.2114040 | -1.3081851 | -1.405590 | -1.503369 | -1.601286 | -1.699115 | -1.796643 | -1.893667 | -1.989999 | -2.085460 | -2.179886 | -2.273123 | -2.365029 | -2.455474 | -2.544338 | -2.631514 |
| Etv4 | 1.063184 | 1.036765 | 1.010452 | 0.9842823 | 0.9582902 | 0.9325114 | 0.9069807 | 0.8817326 | 0.8568014 | 0.8322209 | 0.8080244 | 0.7842452 | 0.7609161 | 0.7380697 | 0.7157382 | 0.6939535 | 0.6727475 | 0.6521517 | 0.6321974 | 0.6129157 | 0.5943376 | 0.5764939 | 0.5594155 | 0.5431329 | 0.5276767 | 0.5130775 | 0.4993659 | 0.4865725 | 0.4747280 | 0.4638631 | 0.4540088 | 0.4451962 | 0.4374566 | 0.4308216 | 0.4253231 | 0.4209932 | 0.4178645 | 0.4159701 | 0.4153434 | 0.4160184 | 0.4180297 | 0.4214123 | 0.4261700 | 0.4321144 | 0.4389864 | 0.4465265 | 0.4544743 | 0.4625686 | 0.4705474 | 0.4781478 | 0.4851058 | 0.4911570 | 0.4960363 | 0.4994786 | 0.5012190 | 0.5009930 | 0.4985377 | 0.4935917 | 0.4858962 | 0.4751955 | 0.4612382 | 0.4437776 | 0.4225732 | 0.3973911 | 0.3680058 | 0.3342007 | 0.2957701 | 0.2525194 | 0.2042676 | 0.1508476 | 0.0921085 | 0.0279162 | -0.0418413 | -0.1170799 | -0.1974353 | -0.2825177 | -0.3719369 | -0.4653039 | -0.5622324 | -0.6623405 | -0.7652522 | -0.8705985 | -0.9780191 | -1.0871631 | -1.1976903 | -1.3092719 | -1.421592 | -1.534346 | -1.647247 | -1.760017 | -1.872396 | -1.984139 | -2.095015 | -2.204807 | -2.313315 | -2.420354 | -2.525752 | -2.629354 | -2.731016 | -2.830610 |
| Foxn3 | 1.179599 | 1.141323 | 1.103284 | 1.0655356 | 1.0281353 | 0.9911373 | 0.9545949 | 0.9185608 | 0.8830866 | 0.8482227 | 0.8140190 | 0.7805244 | 0.7477868 | 0.7158537 | 0.6847715 | 0.6545863 | 0.6253433 | 0.5970874 | 0.5698628 | 0.5437135 | 0.5186830 | 0.4948147 | 0.4721516 | 0.4507368 | 0.4306132 | 0.4118238 | 0.3944119 | 0.3784208 | 0.3638943 | 0.3508766 | 0.3394123 | 0.3295468 | 0.3213263 | 0.3147976 | 0.3100086 | 0.3070086 | 0.3058476 | 0.3065773 | 0.3092509 | 0.3139231 | 0.3206504 | 0.3294913 | 0.3404647 | 0.3533427 | 0.3678057 | 0.3835323 | 0.4001992 | 0.4174805 | 0.4350473 | 0.4525676 | 0.4697061 | 0.4861248 | 0.5014824 | 0.5154354 | 0.5276386 | 0.5377454 | 0.5454093 | 0.5502843 | 0.5520266 | 0.5502957 | 0.5447560 | 0.5350785 | 0.5209422 | 0.5020367 | 0.4780635 | 0.4487388 | 0.4137952 | 0.3729845 | 0.3260798 | 0.2728779 | 0.2132021 | 0.1469041 | 0.0738710 | -0.0057573 | -0.0914859 | -0.1827868 | -0.2791311 | -0.3799923 | -0.4848492 | -0.5931892 | -0.7045105 | -0.8183246 | -0.9341584 | -1.0515564 | -1.1700820 | -1.2893189 | -1.408872 | -1.528370 | -1.647463 | -1.765825 | -1.883155 | -1.999173 | -2.113626 | -2.226282 | -2.336933 | -2.445392 | -2.551495 | -2.655096 | -2.756072 | -2.854316 |
| Zfp281 | 2.378367 | 2.270968 | 2.164729 | 2.0597633 | 1.9561796 | 1.8540826 | 1.7535721 | 1.6547438 | 1.5576888 | 1.4624948 | 1.3692450 | 1.2780194 | 1.1888944 | 1.1019430 | 1.0172356 | 0.9348392 | 0.8548186 | 0.7772360 | 0.7021517 | 0.6296238 | 0.5597091 | 0.4924626 | 0.4279386 | 0.3661900 | 0.3072695 | 0.2512294 | 0.1981216 | 0.1479987 | 0.1009133 | 0.0569192 | 0.0160710 | -0.0215750 | -0.0559612 | -0.0870275 | -0.1147117 | -0.1389488 | -0.1596707 | -0.1768060 | -0.1902791 | -0.2000107 | -0.2059162 | -0.2079065 | -0.2059358 | -0.2002459 | -0.1911817 | -0.1790854 | -0.1642976 | -0.1471587 | -0.1280096 | -0.1071931 | -0.0850543 | -0.0619415 | -0.0382067 | -0.0142057 | 0.0097015 | 0.0331506 | 0.0557733 | 0.0771978 | 0.0970487 | 0.1149479 | 0.1305155 | 0.1433708 | 0.1531329 | 0.1594227 | 0.1618639 | 0.1600845 | 0.1537191 | 0.1424102 | 0.1258110 | 0.1035865 | 0.0754170 | 0.0409995 | 0.0000550 | -0.0474449 | -0.1011638 | -0.1607271 | -0.2257548 | -0.2958626 | -0.3706648 | -0.4497757 | -0.5328118 | -0.6193930 | -0.7091449 | -0.8016993 | -0.8966964 | -0.9937853 | -1.092625 | -1.192887 | -1.294252 | -1.396416 | -1.499085 | -1.601981 | -1.704839 | -1.807406 | -1.909446 | -2.010734 | -2.111059 | -2.210227 | -2.308052 | -2.404366 |
| Thap2 | 2.355146 | 2.240364 | 2.127227 | 2.0158548 | 1.9063593 | 1.7988465 | 1.6934154 | 1.5901587 | 1.4891629 | 1.3905090 | 1.2942724 | 1.2005237 | 1.1093286 | 1.0207485 | 0.9348408 | 0.8516593 | 0.7712547 | 0.6936744 | 0.6189638 | 0.5471658 | 0.4783216 | 0.4124712 | 0.3496534 | 0.2899066 | 0.2332688 | 0.1797783 | 0.1294740 | 0.0823957 | 0.0385847 | -0.0019159 | -0.0390609 | -0.0728020 | -0.1030883 | -0.1298648 | -0.1530728 | -0.1726486 | -0.1885238 | -0.2006239 | -0.2088686 | -0.2131705 | -0.2134347 | -0.2095581 | -0.2014833 | -0.1894673 | -0.1738806 | -0.1550911 | -0.1334661 | -0.1093741 | -0.0831869 | -0.0552805 | -0.0260369 | 0.0041555 | 0.0349004 | 0.0657941 | 0.0964242 | 0.1263707 | 0.1552054 | 0.1824932 | 0.2077927 | 0.2306574 | 0.2506374 | 0.2672809 | 0.2801367 | 0.2887565 | 0.2926974 | 0.2915251 | 0.2848172 | 0.2721667 | 0.2531855 | 0.2275086 | 0.1947980 | 0.1547466 | 0.1070875 | 0.0518572 | -0.0104773 | -0.0794007 | -0.1543888 | -0.2349124 | -0.3204412 | -0.4104481 | -0.5044119 | -0.6018212 | -0.7021766 | -0.8049936 | -0.9098047 | -1.0161612 | -1.123635 | -1.231819 | -1.340329 | -1.448806 | -1.556911 | -1.664333 | -1.770781 | -1.875992 | -1.979723 | -2.081755 | -2.181891 | -2.279955 | -2.375792 | -2.469266 |
| Etv5 | 2.670575 | 2.537633 | 2.406735 | 2.2780114 | 2.1515866 | 2.0275743 | 1.9060801 | 1.7872017 | 1.6710292 | 1.5576448 | 1.4471241 | 1.3395358 | 1.2349424 | 1.1334005 | 1.0349614 | 0.9396712 | 0.8475717 | 0.7587005 | 0.6730915 | 0.5907756 | 0.5117808 | 0.4361332 | 0.3638567 | 0.2949744 | 0.2295082 | 0.1674801 | 0.1089119 | 0.0538264 | 0.0022472 | -0.0458000 | -0.0902877 | -0.1311854 | -0.1684598 | -0.2020734 | -0.2319847 | -0.2581472 | -0.2805091 | -0.2990122 | -0.3135921 | -0.3241766 | -0.3306858 | -0.3330307 | -0.3311630 | -0.3253228 | -0.3158517 | -0.3030863 | -0.2873597 | -0.2690041 | -0.2483523 | -0.2257394 | -0.2015044 | -0.1759908 | -0.1495482 | -0.1225325 | -0.0953067 | -0.0682408 | -0.0417123 | -0.0161053 | 0.0081894 | 0.0307755 | 0.0512522 | 0.0692152 | 0.0842586 | 0.0959768 | 0.1039662 | 0.1078280 | 0.1071706 | 0.1016125 | 0.0907855 | 0.0743380 | 0.0519382 | 0.0232782 | -0.0119183 | -0.0536628 | -0.1015864 | -0.1552767 | -0.2143118 | -0.2782633 | -0.3466996 | -0.4191885 | -0.4953005 | -0.5746108 | -0.6567021 | -0.7411665 | -0.8276076 | -0.9156420 | -1.004901 | -1.095033 | -1.185700 | -1.276586 | -1.367392 | -1.457836 | -1.547657 | -1.636615 | -1.724486 | -1.811066 | -1.896172 | -1.979636 | -2.061309 | -2.141059 |
| Pias4 | 2.438095 | 2.339052 | 2.240891 | 2.1437030 | 2.0475745 | 1.9525903 | 1.8588322 | 1.7663788 | 1.6753061 | 1.5856872 | 1.4975928 | 1.4110911 | 1.3262478 | 1.2431264 | 1.1617881 | 1.0822921 | 1.0046958 | 0.9290546 | 0.8554223 | 0.7838513 | 0.7143924 | 0.6470953 | 0.5820085 | 0.5191796 | 0.4586554 | 0.4004821 | 0.3447053 | 0.2913704 | 0.2405226 | 0.1922072 | 0.1464695 | 0.1033555 | 0.0629115 | 0.0251847 | -0.0097768 | -0.0419238 | -0.0712057 | -0.0975704 | -0.1209639 | -0.1413304 | -0.1586117 | -0.1727472 | -0.1837101 | -0.1916863 | -0.1969373 | -0.1997219 | -0.2002963 | -0.1989147 | -0.1958304 | -0.1912957 | -0.1855628 | -0.1788840 | -0.1715118 | -0.1636996 | -0.1557014 | -0.1477720 | -0.1401673 | -0.1331438 | -0.1269588 | -0.1218702 | -0.1181360 | -0.1160139 | -0.1157616 | -0.1176352 | -0.1218896 | -0.1287774 | -0.1385483 | -0.1514484 | -0.1677192 | -0.1875969 | -0.2113114 | -0.2390853 | -0.2711300 | -0.3074919 | -0.3479733 | -0.3923534 | -0.4404095 | -0.4919173 | -0.5466523 | -0.6043899 | -0.6649065 | -0.7279799 | -0.7933903 | -0.8609202 | -0.9303555 | -1.0014859 | -1.074105 | -1.148011 | -1.223007 | -1.298900 | -1.375505 | -1.452640 | -1.530131 | -1.607807 | -1.685505 | -1.763069 | -1.840347 | -1.917194 | -1.993472 | -2.069046 |
| Etv1 | 2.620729 | 2.496198 | 2.373705 | 2.2533622 | 2.1352699 | 2.0195224 | 1.9062057 | 1.7953982 | 1.6871710 | 1.5815884 | 1.4787079 | 1.3785811 | 1.2812533 | 1.1867649 | 1.0951506 | 1.0064410 | 0.9206622 | 0.8378364 | 0.7579825 | 0.6811163 | 0.6072511 | 0.5363980 | 0.4685665 | 0.4037645 | 0.3419993 | 0.2832775 | 0.2276057 | 0.1749910 | 0.1254411 | 0.0789650 | 0.0355733 | -0.0047214 | -0.0419040 | -0.0759563 | -0.1068571 | -0.1345809 | -0.1590984 | -0.1803753 | -0.1983718 | -0.2130427 | -0.2243362 | -0.2321937 | -0.2365906 | -0.2377420 | -0.2359461 | -0.2314952 | -0.2246776 | -0.2157790 | -0.2050843 | -0.1928790 | -0.1794500 | -0.1650868 | -0.1500821 | -0.1347325 | -0.1193386 | -0.1042052 | -0.0896414 | -0.0759600 | -0.0634772 | -0.0525119 | -0.0433845 | -0.0364160 | -0.0319263 | -0.0302328 | -0.0316487 | -0.0364806 | -0.0450264 | -0.0575732 | -0.0743940 | -0.0957459 | -0.1218663 | -0.1529707 | -0.1892458 | -0.2306636 | -0.2768914 | -0.3275637 | -0.3823090 | -0.4407531 | -0.5025216 | -0.5672427 | -0.6345493 | -0.7040812 | -0.7754872 | -0.8484270 | -0.9225722 | -0.9976085 | -1.073236 | -1.149171 | -1.225145 | -1.300909 | -1.376228 | -1.450888 | -1.524690 | -1.597453 | -1.669015 | -1.739227 | -1.807961 | -1.875100 | -1.940546 | -2.004212 |
| Sall3 | 2.500433 | 2.389266 | 2.279301 | 2.1706518 | 2.0634286 | 1.9577361 | 1.8536742 | 1.7513385 | 1.6508199 | 1.5522049 | 1.4555761 | 1.3610116 | 1.2685858 | 1.1783694 | 1.0904296 | 1.0048302 | 0.9216320 | 0.8408927 | 0.7626676 | 0.6870095 | 0.6139689 | 0.5435947 | 0.4759339 | 0.4110323 | 0.3489344 | 0.2896842 | 0.2333249 | 0.1798997 | 0.1294517 | 0.0820247 | 0.0376628 | -0.0035884 | -0.0416824 | -0.0765706 | -0.1082024 | -0.1365249 | -0.1614825 | -0.1830160 | -0.2010631 | -0.2155573 | -0.2264277 | -0.2335987 | -0.2370338 | -0.2369554 | -0.2336781 | -0.2275122 | -0.2187658 | -0.2077453 | -0.1947565 | -0.1801061 | -0.1641016 | -0.1470529 | -0.1292720 | -0.1110740 | -0.0927769 | -0.0747019 | -0.0571734 | -0.0405188 | -0.0250681 | -0.0111534 | 0.0008916 | 0.0107322 | 0.0180340 | 0.0224635 | 0.0236898 | 0.0213853 | 0.0152278 | 0.0049014 | -0.0099010 | -0.0294764 | -0.0541096 | -0.0840711 | -0.1196112 | -0.1607620 | -0.2072375 | -0.2587186 | -0.3148811 | -0.3753973 | -0.4399372 | -0.5081708 | -0.5797692 | -0.6544059 | -0.7317584 | -0.8115093 | -0.8933473 | -0.9769685 | -1.062077 | -1.148386 | -1.235620 | -1.323510 | -1.411801 | -1.500250 | -1.588623 | -1.676701 | -1.764274 | -1.851147 | -1.937135 | -2.022066 | -2.105781 | -2.188132 |
| Zfp422 | 1.693086 | 1.661176 | 1.629326 | 1.5975225 | 1.5657528 | 1.5340037 | 1.5022623 | 1.4705157 | 1.4387514 | 1.4069568 | 1.3751196 | 1.3432274 | 1.3112681 | 1.2792297 | 1.2471003 | 1.2148682 | 1.1825217 | 1.1500494 | 1.1174398 | 1.0846819 | 1.0517646 | 1.0186768 | 0.9854079 | 0.9519472 | 0.9182842 | 0.8844087 | 0.8503104 | 0.8159793 | 0.7814056 | 0.7465795 | 0.7114917 | 0.6761326 | 0.6404932 | 0.6045645 | 0.5683376 | 0.5318039 | 0.4949549 | 0.4577825 | 0.4202785 | 0.3824350 | 0.3442446 | 0.3056996 | 0.2667986 | 0.2275747 | 0.1880730 | 0.1483382 | 0.1084146 | 0.0683457 | 0.0281745 | -0.0120565 | -0.0523054 | -0.0925310 | -0.1326925 | -0.1727500 | -0.2126639 | -0.2523953 | -0.2919059 | -0.3311579 | -0.3701144 | -0.4087387 | -0.4469949 | -0.4848475 | -0.5222617 | -0.5592031 | -0.5956380 | -0.6315330 | -0.6668553 | -0.7015727 | -0.7356531 | -0.7690652 | -0.8017779 | -0.8337606 | -0.8649834 | -0.8954397 | -0.9251577 | -0.9541682 | -0.9825015 | -1.0101875 | -1.0372556 | -1.0637349 | -1.0896541 | -1.1150416 | -1.1399253 | -1.1643329 | -1.1882916 | -1.2118285 | -1.234970 | -1.257743 | -1.280174 | -1.302288 | -1.324110 | -1.345667 | -1.366983 | -1.388083 | -1.408991 | -1.429733 | -1.450331 | -1.470811 | -1.491194 | -1.511507 |
| Lef1 | 1.982573 | 1.930623 | 1.879136 | 1.8281018 | 1.7775128 | 1.7273596 | 1.6776339 | 1.6283274 | 1.5794319 | 1.5309395 | 1.4828427 | 1.4351340 | 1.3878059 | 1.3408515 | 1.2942639 | 1.2480362 | 1.2021620 | 1.1566348 | 1.1114485 | 1.0665971 | 1.0220746 | 0.9778754 | 0.9339939 | 0.8904248 | 0.8471628 | 0.8042029 | 0.7615402 | 0.7191700 | 0.6770875 | 0.6352884 | 0.5937684 | 0.5525232 | 0.5115488 | 0.4708413 | 0.4303970 | 0.3902122 | 0.3502835 | 0.3106074 | 0.2711806 | 0.2320002 | 0.1930630 | 0.1543661 | 0.1159097 | 0.0777097 | 0.0397876 | 0.0021637 | -0.0351423 | -0.0721118 | -0.1087270 | -0.1449708 | -0.1808270 | -0.2162803 | -0.2513161 | -0.2859205 | -0.3200804 | -0.3537834 | -0.3870177 | -0.4197723 | -0.4520368 | -0.4838013 | -0.5150567 | -0.5457942 | -0.5760057 | -0.6056837 | -0.6348210 | -0.6634110 | -0.6914475 | -0.7189245 | -0.7458368 | -0.7721793 | -0.7979472 | -0.8231361 | -0.8477420 | -0.8717721 | -0.8952492 | -0.9181971 | -0.9406386 | -0.9625959 | -0.9840906 | -1.0051435 | -1.0257748 | -1.0460043 | -1.0658510 | -1.0853335 | -1.1044698 | -1.1232775 | -1.141773 | -1.159974 | -1.177896 | -1.195555 | -1.212965 | -1.230142 | -1.247101 | -1.263855 | -1.280417 | -1.296802 | -1.313022 | -1.329089 | -1.345017 | -1.360817 |
write.table(heatmap_matrix_q_value_0.01, file = file.path(tables_directory, "4-forebrain_astro_ependymal_joint_cortex_cluster_20_2_12_23-significant_transcription_factors_diff_test_analysis_qval_0.01_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)2.2.2.1.3 Plotting of transcription factors differentially expressed in pseudotime
2.2.2.1.3.1 Top 10 differentially expressed genes (q value < 5*10^-5)
transcription_factors_table_q_value_5_10_minus_5_ordered_qval <- arrange(transcription_factors_table_q_value_5_10_minus_5, qval)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[1]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[2]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[3]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[4]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[5]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[6]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[7]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[8]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[9]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[10]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
2.3 Selected genes
# Genes of interest.
genes_of_interest <- c("Aqp4", "Fabp7", "Foxj1", "Nes", "Top2a", "Aldoc")
# Remove genes of interest not present in Seurat dataset
genes_not_present <- genes_of_interest[!genes_of_interest %in% rownames(seurat@data)]
genes_of_interest <- genes_of_interest[!genes_of_interest %in% genes_not_present]
if(length(genes_not_present != 0)) {
print(paste0("The following genes were not present in the Seurat object", genes_not_present))
}
diff_test_res <- differentialGeneTest(monocle[genes_of_interest],
fullModelFormulaStr = "~sm.ns(Pseudotime)")
sig_gene_names <- row.names(subset(diff_test_res, qval < 0.1))plot_pseudotime_heatmap(monocle[genes_of_interest,],
num_clusters = 1,
cores = 1,
show_rownames = T)
2.3.1 Genes in pseudotime, single branch (Selected genes)
p <- plot_genes_in_pseudotime(monocle[genes_of_interest,], color_by="cluster") + scale_color_manual(values=colours)
p <- p %>% remove_geom("point")
p <- p %>% remove_geom("Line")
p <- p %>% + geom_line(aes(x = Pseudotime, y = expectation), size=1)
show(p)
2.3.2 Genes in pseudotime with branches (Selected genes)
p <- plot_genes_branched_pseudotime(monocle[genes_of_interest,], color_by="cluster") + scale_color_manual(values=colours)
show(p)
p <- p %>% remove_geom("point")
show(p)
3 Seurat tSNE plots
p <- cytokit::tsne(seurat, label=FALSE)
show(p)
p <- tsne_plot_clusters_highlighted(seurat, selected_clusters, legend=TRUE)
show(p)
p <- p + theme(legend.position = "none")
show(p)
p <- tsne_plot_clusters_highlighted_with_pseudotime(seurat, monocle, selected_clusters, legend=TRUE)
show(p)
p <- p + theme(legend.position = "none")
show(p)
4 Save monocle object to directory, and write pseudotime of cells to table.
save(monocle, file=file.path(monocle_objects_directory, "4-forebrain_astro_ependymal_joint_cortex_cluster_20_2_12_23.Rda"))
cells_pseudotime <- pData(monocle) %>% select(cell, Pseudotime) %>% rename(pseudotime=Pseudotime)
write.table(cells_pseudotime, file.path(tables_directory, "4-forebrain_astro_ependymal_joint_cortex_cluster_20_2_12_23_cell_pseudotime.txt"), sep="\t", quote=FALSE, row.names=FALSE)5 Session info
sessionInfo()## R version 3.5.0 (2018-04-23)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
##
## Matrix products: default
## BLAS/LAPACK: /var/chroots/hydraex-centos-7/usr/lib64/R/lib/libRblas.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] splines stats4 parallel stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] viridis_0.5.1 viridisLite_0.3.0 forcats_0.4.0
## [4] stringr_1.4.0 dplyr_0.8.0.1 purrr_0.3.0
## [7] tidyr_0.8.2 tibble_2.0.1 tidyverse_1.2.1
## [10] Seurat_2.3.4 cowplot_0.9.4 R.utils_2.8.0
## [13] R.oo_1.22.0 R.methodsS3_1.7.1 readr_1.3.1
## [16] readxl_1.3.0 patchwork_0.0.1 monocle_2.10.1
## [19] DDRTree_0.1.5 irlba_2.3.3 VGAM_1.1-1
## [22] Biobase_2.42.0 BiocGenerics_0.28.0 Matrix_1.2-15
## [25] kableExtra_1.0.1 ggedit_0.3.0 ggplot2_3.1.0
## [28] cytokit_0.6.0 pheatmap_1.0.12 colorRamps_2.3
##
## loaded via a namespace (and not attached):
## [1] snow_0.4-3 backports_1.1.3 Hmisc_4.2-0
## [4] plyr_1.8.4 igraph_1.2.4 lazyeval_0.2.1
## [7] densityClust_0.3 fastICA_1.2-1 digest_0.6.18
## [10] foreach_1.4.4 htmltools_0.3.6 lars_1.2
## [13] gdata_2.18.0 magrittr_1.5 checkmate_1.9.1
## [16] cluster_2.0.7-1 mixtools_1.1.0 ROCR_1.0-7
## [19] limma_3.38.3 modelr_0.1.3 matrixStats_0.54.0
## [22] docopt_0.6.1 colorspace_1.4-0 ggrepel_0.8.0
## [25] rvest_0.3.2 haven_2.0.0 xfun_0.4
## [28] sparsesvd_0.1-4 crayon_1.3.4 jsonlite_1.6
## [31] survival_2.43-3 zoo_1.8-4 iterators_1.0.10
## [34] ape_5.2 glue_1.3.0 gtable_0.2.0
## [37] webshot_0.5.1 kernlab_0.9-27 prabclus_2.2-7
## [40] DEoptimR_1.0-8 scales_1.0.0 mvtnorm_1.0-8
## [43] bibtex_0.4.2 miniUI_0.1.1.1 Rcpp_1.0.0
## [46] metap_1.1 dtw_1.20-1 xtable_1.8-3
## [49] htmlTable_1.13.1 reticulate_1.11.1 foreign_0.8-71
## [52] bit_1.1-14 proxy_0.4-22 mclust_5.4.2
## [55] SDMTools_1.1-221 Formula_1.2-3 tsne_0.1-3
## [58] htmlwidgets_1.3 httr_1.4.0 FNN_1.1.3
## [61] gplots_3.0.1.1 RColorBrewer_1.1-2 shinyAce_0.3.3
## [64] fpc_2.1-11.1 acepack_1.4.1 modeltools_0.2-22
## [67] ica_1.0-2 pkgconfig_2.0.2 flexmix_2.3-14
## [70] nnet_7.3-12 labeling_0.3 tidyselect_0.2.5
## [73] rlang_0.3.1 reshape2_1.4.3 later_0.8.0
## [76] cellranger_1.1.0 munsell_0.5.0 tools_3.5.0
## [79] cli_1.0.1 generics_0.0.2 broom_0.5.1
## [82] ggridges_0.5.1 evaluate_0.13 shinyBS_0.61
## [85] yaml_2.2.0 npsurv_0.4-0 knitr_1.21
## [88] bit64_0.9-7 fitdistrplus_1.0-14 robustbase_0.93-3
## [91] caTools_1.17.1.1 randomForest_4.6-14 RANN_2.6.1
## [94] pbapply_1.4-0 nlme_3.1-137 mime_0.6
## [97] slam_0.1-44 xml2_1.2.0 hdf5r_1.0.0
## [100] compiler_3.5.0 rstudioapi_0.9.0 png_0.1-7
## [103] lsei_1.2-0 stringi_1.3.1 highr_0.7
## [106] lattice_0.20-35 trimcluster_0.1-2.1 HSMMSingleCell_1.2.0
## [109] pillar_1.3.1 combinat_0.0-8 Rdpack_0.10-1
## [112] lmtest_0.9-36 data.table_1.12.0 bitops_1.0-6
## [115] gbRd_0.4-11 httpuv_1.4.5.1 R6_2.4.0
## [118] latticeExtra_0.6-28 promises_1.0.1 KernSmooth_2.23-15
## [121] gridExtra_2.3 codetools_0.2-15 MASS_7.3-51.1
## [124] gtools_3.8.1 assertthat_0.2.0 withr_2.1.2
## [127] qlcMatrix_0.9.7 diptest_0.75-7 doSNOW_1.0.16
## [130] hms_0.4.2 grid_3.5.0 rpart_4.1-13
## [133] class_7.3-14 rmarkdown_1.11 segmented_0.5-3.0
## [136] Rtsne_0.15 lubridate_1.7.4 shiny_1.2.0
## [139] base64enc_0.1-3